Import data

Sunday, August 24, 2025

Microbiome data science workflow

Microbiome data science workflow

Importers and converters

  • mia includes importers and converters for standard data formats
    • Importer: Import file
    • Converter: Convert R object to other format
  • You can also create TreeSE object manually

Open databases

Data resource Package # studies or datasets # samples
Curated metagenomic data (Pasolli et al. 2017) curatedMetagenomicData (Pasolli et al. 2017) 93 22,588
HoloFood (Rogers et al. 2025) HoloFoodR (Borman, Sannikov, and Lahti 2025) - 9,990
MGnify (Gurbich et al. 2023) MGnifyR (Borman, Allen, and Lahti 2025) 5129 616,138
microbiomeDataSets (Lahti, Ernst, and Shetty 2025) microbiomeDataSets (Lahti, Ernst, and Shetty 2025) 6 19,100

Demonstration

library(mia)

tse <- importBIOM("file_path.biom")
print(tse)
class: TreeSummarizedExperiment 
dim: 19216 26 
metadata(0):
assays(1): counts
rownames(19216): 549322 522457 ... 200359 271582
rowData names(7): Kingdom Phylum ... Genus Species
colnames(26): CL3 CC1 ... Even2 Even3
colData names(7): X.SampleID Primer ... SampleType Description
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
rowLinks: a LinkDataFrame (19216 rows)
rowTree: 1 phylo tree(s) (19216 leaves)
colLinks: NULL
colTree: NULL

Exercises

From OMA online book, Chapter 4: Import

  • Exercise 2

References

https://microbiome.github.io/

Borman, Tuomas, Ben Allen, and Leo Lahti. 2025. MGnifyR: R Interface to EBI MGnify Metagenomics Resource. https://github.com/EBI-Metagenomics/MGnifyR.
Borman, Tuomas, Artur Sannikov, and Leo Lahti. 2025. HoloFoodR: R Interface to EBI HoloFood Resource. https://github.com/EBI-Metagenomics/HoloFoodR.
Gurbich, Tatiana A., Alexandre Almeida, Martin Beracochea, Tony Burdett, Josephine Burgin, Guy Cochrane, Shriya Raj, et al. 2023. “MGnify Genomes: A Resource for Biome-Specific Microbial Genome Catalogues.” Journal of Molecular Biology, Computation resources for molecular biology, 435 (14): 168016. https://doi.org/10.1016/j.jmb.2023.168016.
Lahti, Leo, Felix G. M. Ernst, and Sudarshan Shetty. 2025. microbiomeDataSets: Experiment Hub Based Microbiome Datasets. https://doi.org/10.18129/B9.bioc.microbiomeDataSets.
Pasolli, Edoardo, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, et al. 2017. “Accessible, Curated Metagenomic Data Through ExperimentHub.” Nature Methods 14 (11): 1023–24. https://doi.org/10.1038/nmeth.4468.
Rogers, Alexander B, Varsha Kale, Germana Baldi, Antton Alberdi, M Thomas P Gilbert, Dipayan Gupta, Morten T Limborg, et al. 2025. “HoloFood Data Portal: Holo-Omic Datasets for Analysing Host–Microbiota Interactions in Animal Production.” Database (Oxford) 2025: baae112. https://doi.org/10.1093/database/baae112.